Megaplasmid Dissemination in Multidrug-Resistant Salmonella Serotypes from Backyard and Commercial Broiler Production Systems in the Southeastern United States

Over the past decade, there has been a rise in U.S. backyard poultry ownership, raising concern for residential area antimicrobial-resistant (AMR) Salmonella contamination. This study aims to lay the groundwork to better understand the persistence of AMR Salmonella in residential broiler production systems and make comparisons with commercial systems. Ten backyard and 10 commercial farms were sampled at three time points across bird production. Both fecal (n = 10) and environmental (soil, n = 5, litter/compost, n = 5, feeder, and waterer swabs, n = 6) samples were collected at each visit on days 10, 31, and 52 of production for backyard farms and days 10, 24, and 38 of production for commercial farms. AMR Salmonella was characterized phenotypically by broth microdilution and genotypically by whole-genome sequencing. Overall, Salmonella was more prevalent in commercial farm samples (52.31%) over backyard farms (19.10%). Kentucky (sequence type (ST) 152) was the most common serotype found in both backyard and commercial farms. Multidrug-resistant (MDR, resistance to ≥3 or more antimicrobial classes) isolates were found in both production systems, while ciprofloxacin- and nalidixic acid-resistant and intermediate isolates were more prevalent in commercial (33%) than backyard samples (1%). Plasmids that have been associated with MDR were found in Kentucky and Infantis isolates, particularly IncFIB(K)_1_Kpn3 megaplasmid (Infantis). Our study emphasizes the need to understand the selection pressures in disseminating megaplasmids in MDR Salmonella in distinct broiler production systems.

Tracking the Transmission of Antimicrobial-Resistant Non-O157 Escherichia coli and Salmonella Isolates at the Interface of Food Animals and Fresh Produce from Agriculture Operations Using Whole-Genome Sequencing

An increasing number of outbreaks are caused by foodborne pathogens such as Escherichia coli and Salmonella, which often harbor antimicrobial resistance (AMR) genes. We previously demonstrated the transmission of pathogens from animal operations to produce fields on sustainable farms, which illustrated an urgent need to develop and implement novel prevention methods and remediation practices such as the vegetative buffer zone (VBZ) to prevent this movement. The focus of this study was to use whole-genome sequencing (WGS) to characterize the AMR, virulence, and single-nucleotide polymorphism profile of 15 Salmonella and 128 E. coli isolates collected from small-scale dairy and poultry farms on a research station in North Carolina. Phenotypically, seven E. coli and three Salmonella isolates displayed resistance to antibiotics such as tetracycline (n = 4), ampicillin (n = 4), nalidixic acid (n = 3), chloramphenicol (n = 2), sulfisoxazole (n = 1), and streptomycin (n = 1). A single E. coli isolate was found to be resistant to five different antibiotic class types and possessed the bla_TEM-150 resistance gene. Virulence genes that facilitate toxin production and cell invasion were identified. Mauve analysis of the E. coli isolates identified seven clusters (dairy-six and poultry-one) indicating that transmission is occurring from animal operations to fresh produce fields and the surrounding environment when the VBZ is denudated. This suggests that the VBZ is a useful barrier to reducing the transmission of enteric pathogens in agricultural systems. Our study demonstrates the prevalence of AMR and virulence genes on small-scale sustainable farms and highlights the advantage of using WGS to assess the impact of the VBZ to reduce the transmission of E. coli and Salmonella.

Antimicrobial resistance and virulence factors profile of Salmonella spp. and Escherichia coli isolated from different environments exposed to anthropogenic activity

OBJECTIVE

The study aimed to identify the antimicrobial resistance (AMR) determinants and virulence factors in Salmonella spp. and Escherichia coli recovered from different anthropogenic areas in North Carolina.

METHODS

Soil samples were collected from different anthropogenic areas, urban and natural. The minimum inhibitory concentration (MIC) was determined by using the broth microdilution method. Whole-genome sequencing (WGS) and analysis were done to identify the AMR determinants and virulence factors.

RESULTS

A higher prevalence of Salmonella spp. and E. coli was detected in the urban environment. The Salmonella spp. isolates showed resistance to sulfisoxazole and streptomycin, whereas E. coli was resistant to sulfisoxazole, cefoxitin and ampicillin. Salmonella serotypes Schwarzengrund and Mississippi were identified based on WGS analysis. Aminoglycoside resistance genes and IncFIB and IncFIC(FII) plasmids were detected among Salmonella spp. In general, E. coli was predominated by isolates from phylogroups B1, B2 and D. The multidrug transporter mdfA gene was detected in most of the E. coli from both the urban (100%) and natural (84.5%) environments. The FosA7 gene was detected in an isolate from a residential yard. The pCoo and pB171 plasmids were detected in an urban environment; col(156) and pHN7A8 plasmids were detected in natural environments.

CONCLUSIONS

The detection of AMR determinants and virulence factors in these bacteria is significant in understanding the occurrence and even the development of AMR. The presence of these determinants in different anthropogenic areas suggests the need to conduct longitudinal studies for comparing the profile of pathogens across different environments.

Extended-spectrum ß-lactamase-producing Escherichia coli among humans, chickens and poultry environments in Abuja, Nigeria

BACKGROUND

Globally, chicken is known to be a reservoir for the spread of antimicrobial resistance genes to humans. In Nigeria, antimicrobial drugs are readily accessible for use in poultry production, either for preventive or therapeutic purposes. Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) are transmissible to humans because of their zoonotic potentials. People working very closely with chickens either on farms or markets are at greater risk. The aim of this study was to investigate the prevalence and zoonotic transmission of ESBL-EC among poultry-workers, chickens, and poultry environments in Abuja, Nigeria.

METHODS

We conducted a cross-sectional study among workers, chickens and poultry environment in selected farms/chicken markets in Abuja. Stool, faecal, and environmental samples were collected from apparently healthy workers, chickens, and farm/market environments from December 2018 to April 2019. Data were collected electronically using an open data kit (ODK) installed on a Smartphone. Antimicrobial resistance was determined using broth micro-dilution methods against a panel of 14 antimicrobial agents. We carried out the phenotypic and genotypic characterization of the isolates. Data were analyzed by computing frequencies, proportions and spearman's correlation (ρ).

RESULTS

Of 429 samples, 26.8% (n = 115) were positive for Escherichia coli (E. coli). Of the 115 E. coli isolates, 32.2% (n = 37) were confirmed ESBL producers by phenotypic characterization. Prevalence of ESBL-EC was highest among both poultry-workers (37.8%; n = 14) and chickens (37.8%; n = 14) followed by the environment (24.3%; n = 9). Both human and chicken isolates showed similar patterns of multidrug resistance to tested antimicrobials with a positive correlation (ρ = 0.91). Among ESBL producers, we observed the dissemination of blaCTX-M (10.8%; n = 4) genes. The coexistence of blaCTX-M-15 and blaTEM-1 genes was observed in 8.1% (n = 3) of the isolates, out of which (66.7%; n = 2) were chicken isolates from the farm, while a single human isolate was from the chicken market.

CONCLUSIONS

ESBL-EC isolates were prevalent amongst apparently healthy individuals, chickens and the poultry farm/market environment in Abuja. It is important to educate healthcare workers that people in proximity with poultry are a high-risk group for faecal carriage of ESBL-EC, hence pose a higher risk to the general population for the spread of antimicrobial resistance.

Thermoacoustic contrast of prostate cancer due to heating by very high frequency irradiation

Applying the thermoacoustic (TA) effect to diagnostic imaging was first proposed in the 1980s. The object under test is irradiated by high-power pulses of electromagnetic energy, which heat tissue and cause thermal expansion. Outgoing TA pressure pulses are detected by ultrasound transducers and reconstructed to provide images of the object. The TA contrast mechanism is strongly dependent upon the frequency of the irradiating electromagnetic pulse. When very high frequency (VHF) electromagnetic irradiation is utilized, TA signal production is driven by ionic content. Prostatic fluids contain high levels of ionic metabolites, including citrate, zinc, calcium, and magnesium. Healthy prostate glands produce more ionic metabolites than diseased glands. VHF pulses are therefore expected to generate stronger TA signal in healthy prostate glands than in diseased glands. A benchtop system for performing ex vivo TA computed tomography with VHF energy is described and images are presented. The system utilizes irradiation pulses of 700 ns duration exceeding 20 kW power. Reconstructions frequently visualize anatomic landmarks such as the urethra and verumontanum. TA reconstructions from three freshly excised human prostate glands with little, moderate, and severe cancerous involvement are compared with histology. TA signal strength is negatively correlated with percent cancerous involvement in this small sample size. For the 45 regions of interest analyzed, a reconstruction value of 0.4 mV provides 100% sensitivity but only 29% specificity. This sample size is far too small to draw sweeping conclusions, but the results warrant a larger volume study including comparison of TA images to the gold standard, histology.

Abdominal subcutaneous adipose tissue insulin resistance and lipolysis in patients with non-alcoholic steatohepatitis

BACKGROUND

Systemic insulin resistance (IR) is a primary feature in non-alcoholic steatohepatitis (NASH), however, there remain limited data on tissue-specific insulin sensitivity in vivo.

METHODS

We examined tissue-specific (adipose, muscle and liver) insulin sensitivity and inflammation in 16 European Caucasian patients with biopsy-confirmed NASH and in 15 healthy controls. All underwent a two-step hyperinsulinaemic euglycaemic clamp incorporating stable isotope measurements of carbohydrate and lipid metabolism with concomitant subcutaneous adipose tissue (SAT) microdialysis.

RESULTS

Hepatic and muscle insulin sensitivity were decreased in patients with NASH compared with controls, as demonstrated by reduced suppression of hepatic glucose production and glucose disposal (Gd) rates following insulin infusion. In addition, rates of lipolysis were higher in NASH patients with impaired insulin-mediated suppression of free fatty acid levels. At a tissue specific level, abdominal SAT in patients with NASH was severely insulin resistant, requiring >sixfold more insulin to cause ½-maximal suppression of glycerol release when compared with healthy controls. Furthermore, patients with NASH had significantly higher circulating levels of pro-inflammatory adipocytokines than controls.

CONCLUSION

NASH patients have profound IR in the liver, muscle and in particular adipose tissues. This study represents the first in vivo description of dysfunctional SAT in patients with NASH.

Effectiveness of 0.05% oxymetazoline (Vicks Sinex Micromist®) nasal spray in the treatment of objective nasal congestion demonstrated to 12 h post-administration by magnetic resonance imaging

INTRODUCTION

This study aimed to assess the qualitative and quantitative utility of MRI imaging to illustrate the magnitude and duration of the effect of a standard 100 μg dose of oxymetazoline in a commercially available formulation that also contains aromatic oils.

METHODS

This was a randomized, open label, single dose, parallel group study in 21 adult male and female subjects who reported moderate to severe nasal congestion due to acute upper respiratory tract infection or hay fever. MRI scans were acquired using a 3T Philips Achieva scanner with a 16 channel head receive coil. High resolution MRI scans of the nasal turbinates were obtained immediately prior to dosing (baseline) and at approximately 1, 8, 10, 11, and 12 h after dosing. The efficacy variables of primary interest were inferior turbinate total volume at 8 and 12 h post-dosing. The secondary efficacy variables analysed were inferior turbinate total volume at 1, 10, and 11 h post-dosing, middle turbinate total volume at 1, 8, 10, 11, and 12 h post-dosing.

RESULTS

Changes from baseline volumes measured for the inferior and middle turbinates of subjects receiving the oxymetazoline formulation showed significant (P < 0.05) decreases at all times up to and including 12 h post-administration. No significant decreases from baseline were detected in subjects receiving a sham 'spray' (untreated control - spray bottles with no spray solution). Statistical ANCOVA results of inferior and middle turbinate volume indicated significant differences (P < 0.05) at all measurement points up to and including 12 h post-administration between the oxymetazoline treatment group and the untreated control with the only exception the middle turbinate volume at 10 h (P = 0.0896). The significant changes were likely to be clinically relevant though this was not measured in the study. No AEs were reported during this study and no other safety evaluations were made.

CONCLUSIONS

This study showed that MRI assessment of nasal congestion in human volunteers is a robust, repeatable and viable measurement technique. The application of a 100 μg Vicks Sinex Micromist(®) nasal decongestant (0.05% oxymetazoline solution) delivered a highly significant reduction in inferior and middle turbinate volumes compared with the application of a control, measurable by the MRI method up to and including a 12 h post-dose scan.

Sorafenib for advanced hepatocellular carcinoma (HCC): impact of rationing in the United Kingdom

BACKGROUND

The prognosis for hepatocellular carcinoma (HCC) is dependent upon tumour stage, performance status (PS), severity of underlying liver disease, and the availability of appropriate therapies. The unavailability of sorafenib may have a significantly adverse effect on the prognosis of UK patients with advanced HCC. During the study period, access to sorafenib was at the discretion of local health funding bodies, a process that may delay or deny access to the drug and that remains in place for Wales, Scotland, and Northern Ireland. Here, we attempt to address the impact of this system on patients with advanced HCC in the United Kingdom.

METHODS

This is a retrospective study performed in the two largest specialist hepatobiliary oncology units in the United Kingdom. Funding applications were made to local funding bodies for patients with advanced HCC for whom sorafenib was considered appropriate (advanced HCC not suitable for loco-regional therapies, compensated chronic liver disease, PS 0-2).

RESULTS

A total of 133 applications were made, of which 57 (43%) were approved and 76 (57%) declined. Demographics and prognostic factors were balanced between the two groups. This cohort had a number of adverse prognostic features: patients were predominantly PS 1-2; the majority had multifocal disease with the largest lesion being >5 cm; and macroscopic vascular invasion, metastases, and AFP >,000 ng ml(-1), were each present in one-third of cases. The median time from application to funding decision was 17 days (range 3-260 days). For the primary 'intention-to-treat' analysis, median overall survival was 4.1 months when funding was declined, and 9.5 months when funding was approved (hazard ratio (HR) 0.48; 95% CI 0.3186-0.7267; P=0.0005).

CONCLUSION

These data support the use of sorafenib for patients with advanced HCC as an effective intervention. In the United Kingdom, this applies to a relatively small group of patients, estimated to total ∼800 per year who, unfortunately, do not survive long enough to themselves lobby for the availability of this drug. These data provide a comparison of sorafenib with supportive care and demonstrate the potential detrimental impact on patient outcomes of rationing health-care resources on the basis of cost.

Post-axial polydactyly type A2, overgrowth and autistic traits associated with a chromosome 13q31.3 microduplication encompassing miR-17-92 and GPC5

Genomic rearrangements at chromosome 13q31.3q32.1 have been associated with digital anomalies, dysmorphic features, and variable degree of mental disability. Microdeletions leading to haploinsufficiency of miR17∼92, a cluster of micro RNA genes closely linked to GPC5 in both mouse and human genomes, has recently been associated with digital anomalies in the Feingold like syndrome. Here, we report on a boy with familial dominant post-axial polydactyly (PAP) type A, overgrowth, significant facial dysmorphisms and autistic traits who carries the smallest germline microduplication known so far in that region. The microduplication encompasses the whole miR17∼92 cluster and the first 5 exons of GPC5. This report supports the newly recognized role of miR17∼92 gene dosage in digital developmental anomalies, and suggests a possible role of GPC5 in growth regulation and in cognitive development.

Oral Candida infection and colonization in solid organ transplant recipients

INTRODUCTION

Oral Candida carriage and infection have been reported to be associated with a greater risk for systemic infection in transplant recipients; however, a systematic analysis of the oral Candida titers and species has not been previously conducted. The objectives of this study were to determine the prevalence of oropharyngeal candidiasis, the oral carrier status, Candida titers and species in this population.

METHODS

Ninety kidney and heart transplant subjects and 72 age-matched healthy controls were included. Swabs from the oral mucosa and a standardized amount of unstimulated saliva were plated on Chromagar Candida, and colony-forming units per millilitre were calculated. Initial speciation was based on colony color and was confirmed by standard germ tube, biotyping, or polymerase chain reaction assays.

RESULTS

Infection with C. albicans was detected in seven transplant subjects and none of the controls. The transplant group had significantly higher oral Candida titers than the control group. There were no statistically significant relationships between the dose or type of immunosuppressants and oral Candida titers or infection. A significantly higher percentage of transplant subjects were colonized by more than one species, compared with control subjects. The most frequent species combination in transplant subjects was C. albicans and C. glabrata. C. glabrata was isolated from 13.5% of transplant carriers and none of the controls.

CONCLUSIONS

Increased oral Candida infection and carriage titers were found in the transplant population. Although the majority of transplant patients were colonized by C. albicans, C. glabrata appears to emerge as the second most prevalent species.

The (my)Grid ontology: bioinformatics service discovery

(my)Grid supports in silico experiments in the life sciences, enabling the design and enactment of workflows as well as providing components to assist service discovery, data and metadata management. The (my)Grid ontology is one component in a larger semantic discovery framework for the identification of the highly distributed and heterogeneous bioinformatics services in the public domain. From an initial model of formal OWL-DL semantics throughout, we now adopt a spectrum of expressivity and reasoning for different tasks in service annotation and discovery. Here, we discuss the development and use of the (my)Grid ontology and our experiences in semantic service discovery.

Effects of creating a non-specific, virus-hostile environment in the nasopharynx on symptoms and duration of common cold

The Common Cold remains the most frequent symptomatic viral infection in man. Current best therapies are all symptomatic. New pharmacological therapies are likely to be prescription-bound, and as most Common Cold infections are successfully treated without the intervention of a Physician, there is a need for effective non-prescription therapy options. Aim of this study is to propose a new type of approach, based on the concept of making a hostile biological environment for virus survival and spreading at the point of infection, the nasopharynx. The hypothesis was advanced that infections could be controlled using a physical biological approach to create an environment at the point of infection, that is inhibitory to the survival, and persistence of infecting virus, and of viruses newly released from infected mucosal epithelial cells. A nasal irrigation spray, designed to deliver a low pH gel to the nasal cavity, was developed and tested in this study. The study was a randomised, parallel, double-blind, placebo-controlled evaluation of three formulations of irrigation nasal spray in 441 subjects. The objective was to test whether the formulations reduced Cold severity and Cold duration compared to a placebo nasal spray. Subjects were recruited, and supplied with the product when healthy, and were instructed to begin treating and recording symptom severity once they experienced the "first signs" of a Common Cold. To qualify, subjects had to volunteer that they had at least one of the symptoms: sore/scratchy throat, runny nose or congested nose. The product was used 4 times daily, with at least 4 hours separating each dose, for a maximum of 7 days. Efficacy was assessed by an Interactive Voice Recall System whereby subjects were required to contact the investigation site, by telephone, twice daily when they were asked to assess the severity of their symptoms using a four point ordinal scale where 0 = "absent", and 3 = "severe". The symptoms assessed were sore throat, runny nose, blocked nose, cough and tired/run-down feeling. Two formulations demonstrated significant effects. A hydroxy methyl propyl cellulose based formulation reduced symptom severity compared with placebo by 17% and a Poloxamer based formulation reduced severity by 21%. Duration of illness was reduced with a hydroxy methyl propyl cellulose based formulation by 1.5 days to 2.4 days (according to the dose) and by a Poloxamer based formulation by 2.5 days. Results of this study suggest that the creation of a non virus-specific, inhibitory environment in the nasopharynx holds promise as an effective method of controlling the severity and duration of the Common Cold.